Here we go beyond previous theories to analyze how a simple linear retinal encoding model with different convolutional cell types efficiently encodes naturalistic spatiotemporal movies given a fixed firing rate budget.

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Spatial transcriptomics data is invaluable for understanding the spatial organization of gene expression in tissues. There have been consistent efforts in studying how to effectively utilize the associated spatial information for refining gene expression modeling. We introduce a class of distance-preserving generative models for spatial transcriptomics, which utilizes the provided spatial information to regularize the learned representation space of gene expressions to have a similar pair-wise distance structure. This helps the latent space to capture meaningful encodings of genes in spatial proximity. We carry out theoretical analysis over a tractable loss function for this purpose and formalize the overall learning objective as a regularized evidence lower bound. Our framework grants compatibility with any variational-inference-based generative models for gene expression modeling. Empirically, we validate our proposed method on the mouse brain tissues Visium dataset and observe improved performance with variational autoencoders and scVI used as backbone models.

Classification models for the multivariate time series have gained significant importance in the research community, but not much research has been done on generating adversarial samples for these models. Such samples of adversaries could become a security concern. In this paper, we propose transforming the existing adversarial transformation network (ATN) on a distilled model to attack various multivariate time series classification models. The proposed attack on the classification model utilizes a distilled model as a surrogate that mimics the behavior of the attacked classical multivariate time series classification models. The proposed methodology is tested onto 1-Nearest Neighbor Dynamic Time Warping (1-NN DTW) and a Fully Convolutional Network (FCN), all of which are trained on 18 University of East Anglia (UEA) and University of California Riverside (UCR) datasets. We show both models were susceptible to attacks on all 18 datasets. To the best of our knowledge, adversarial attacks have only been conducted in the domain of univariate time series and have not been conducted on multivariate time series. such an attack on time series classification models has never been done before. Additionally, we recommend future researchers that develop time series classification models to incorporating adversarial data samples into their training data sets to improve resilience on adversarial samples and to consider model robustness as an evaluative metric.

In the teacher-student scenario under the assumption that the teacher's couplings are sparse and the student does not know the graphical structure, the learning curve and order parameters are assessed in the typical case using the replica and cavity methods from statistical mechanics. Our formulation is also applicable to a certain class of cost functions having locality; the standard likelihood does not belong to that class. The derived analytical formulas indicate that the perfect inference of the presence/absence of the teacher's couplings is possible in the thermodynamic limit taking the number of spins N as infinity while keeping the dataset size M proportional to N, as long as α M/N 2. Meanwhile, the formulas also show that the estimated coupling values corresponding to the truly existing ones in the teacher tend to be overestimated in the absolute value, manifesting the presence of estimation bias. These results are considered to be exact in the thermodynamic limit on locally treelike networks, such as the regular random or Erd os-R enyi graphs. Numerical simulation results fully support the theoretical predictions. Additional biases in the estimators on loopy graphs are also discussed. 1 Introduction Inference based on the classical Ising model is called the inverse Ising problem or Boltzmann machine learning, which is attracting more and more attention with the increasing interest in machine learning technologies.

Understanding learning materials (e.g. test questions) is a crucial issue in online learning systems, which can promote many applications in education domain. Unfortunately, many supervised approaches suffer from the problem of scarce human labeled data, whereas abundant unlabeled resources are highly underutilized. To alleviate this problem, an effective solution is to use pre-trained representations for question understanding. However, existing pre-training methods in NLP area are infeasible to learn test question representations due to several domain-specific characteristics in education. First, questions usually comprise of heterogeneous data including content text, images and side information. Second, there exists both basic linguistic information as well as domain logic and knowledge. To this end, in this paper, we propose a novel pre-training method, namely QuesNet, for comprehensively learning question representations. Specifically, we first design a unified framework to aggregate question information with its heterogeneous inputs into a comprehensive vector. Then we propose a two-level hierarchical pre-training algorithm to learn better understanding of test questions in an unsupervised way. Here, a novel holed language model objective is developed to extract low-level linguistic features, and a domain-oriented objective is proposed to learn high-level logic and knowledge. Moreover, we show that QuesNet has good capability of being fine-tuned in many question-based tasks. We conduct extensive experiments on large-scale real-world question data, where the experimental results clearly demonstrate the effectiveness of QuesNet for question understanding as well as its superior applicability.

Exact structured inference with neural network scoring functions is computationally challenging but several methods have been proposed for approximating inference. One approach is to perform gradient descent with respect to the output structure directly (Belanger and McCallum, 2016). Another approach, proposed recently, is to train a neural network (an "inference network") to perform inference (Tu and Gimpel, 2018). In this paper, we compare these two families of inference methods on three sequence labeling datasets. We choose sequence labeling because it permits us to use exact inference as a benchmark in terms of speed, accuracy, and search error. Across datasets, we demonstrate that inference networks achieve a better speed/accuracy/search error trade-off than gradient descent, while also being faster than exact inference at similar accuracy levels. We find further benefit by combining inference networks and gradient descent, using the former to provide a warm start for the latter.

One of the most striking aspects of early visual processing in the retina is the immediate parcellation of visual information into multiple parallel pathways, formed by different retinal ganglion cell types each tiling the entire visual field. Existing theories of efficient coding have been unable to account for the functional advantages of such cell-type diversity in encoding natural scenes. Here we go beyond previous theories to analyze how a simple linear retinal encoding model with different convolutional cell types efficiently encodes naturalistic spatiotemporal movies given a fixed firing rate budget. We find that optimizing the receptive fields and cell densities of two cell types makes them match the properties of the two main cell types in the primate retina, midget and parasol cells, in terms of spatial and temporal sensitivity, cell spacing, and their relative ratio. Moreover, our theory gives a precise account of how the ratio of midget to parasol cells decreases with retinal eccentricity. Also, we train a nonlinear encoding model with a rectifying nonlinearity to efficiently encode naturalistic movies, and again find emergent receptive fields resembling those of midget and parasol cells that are now further subdivided into ON and OFF types. Thus our work provides a theoretical justification, based on the efficient coding of natural movies, for the existence of the four most dominant cell types in the primate retina that together comprise 70% of all ganglion cells.

One of the most striking aspects of early visual processing in the retina is the immediate parcellation of visual information into multiple parallel pathways, formed by different retinal ganglion cell types each tiling the entire visual field. Existing theories of efficient coding have been unable to account for the functional advantages of such cell-type diversity in encoding natural scenes. Here we go beyond previous theories to analyze how a simple linear retinal encoding model with different convolutional cell types efficiently encodes naturalistic spatiotemporal movies given a fixed firing rate budget. We find that optimizing the receptive fields and cell densities of two cell types makes them match the properties of the two main cell types in the primate retina, midget and parasol cells, in terms of spatial and temporal sensitivity, cell spacing, and their relative ratio. Moreover, our theory gives a precise account of how the ratio of midget to parasol cells decreases with retinal eccentricity. Also, we train a nonlinear encoding model with a rectifying nonlinearity to efficiently encode naturalistic movies, and again find emergent receptive fields resembling those of midget and parasol cells that are now further subdivided into ON and OFF types. Thus our work provides a theoretical justification, based on the efficient coding of natural movies, for the existence of the four most dominant cell types in the primate retina that together comprise 70% of all ganglion cells.

Activity of a neuron, even in the early sensory areas, is not simply a function of its local receptive field or tuning properties, but depends on global context of the stimulus, as well as the neural context. This suggests the activity of the surrounding neurons and global brain states can exert considerable influence on the activity of a neuron. In this paper we implemented an L1 regularized point process model to assess the contribution of multiple factors to the firing rate of many individual units recorded simultaneously from V1 with a 96-electrode "Utah" array. We found that the spikes of surrounding neurons indeed provide strong predictions of a neuron's response, in addition to the neuron's receptive field transfer function. We also found that the same spikes could be accounted for with the local field potentials, a surrogate measure of global network states. This work shows that accounting for network fluctuations can improve estimates of single trial firing rate and stimulus-response transfer functions.